The influenza A virus represents one of the greatest global human health risks. Although vaccines provide significant protection from seasonal flu infections they still account for an estimated 36,000 deaths and 200,000 hospitalizations per year in the US alone. Furthermore, the inherent time involved in development, production and distribution of vaccines limits their potential efficacy against rapidly emerging outbreaks. Two classes of drugs have been approved for influenza prophylaxis and treatment. Alarmingly, the past decade has witnessed the emergence of drug resistance as well as recent outbreaks of pandemic (H1N1) and highly pathogenic (H5N1) strains of influenza A. Optimally, as adopted for the treatment of other viral diseases, combination drug therapies would be used to provide the most effective prophylaxis and treatment and to inhibit the emergence of additional drug- resistances. However, only one class of drug (neuraminidase inhibitors) is currently available; amantadine-resistance has become so widespread the amantadanes have become ineffective. There is currently an urgent need for new and more effective therapeutic strategies. Here we provide an innovative approach to identify novel inhibitors of the assembly of the influenza A RNA polymerase subunits PA and PB1. These subunits associate at highly conserved interaction sites through packing of short helical segments. Interestingly, inhibiting PA-PB1 association by mutagenesis or with peptides blocks viral replication and co-crystal structure indicates the binding should be amenable to small- molecule inhibitors. We have developed a novel cell and fluorescence-based PA-PB1 subunit association assay for high-throughput-screening of chemical libraries and confirmation of virtual hit compounds. Using this approach we propose to identify inhibitory compounds acting at a novel influenza A target site for the development of new broad-spectrum influenza drug therapies.